Publications from 2020 to Present

2025

Fung HYJ, Jiou J, Niesman AB, Bernardes NE, Chook YM. "Nap1 and Kap114 co-chaperone H2A-H2B and facilitate targeted histone release in the nucleus." J Cell Biol. 2025 Jan 6;224(1):e202408193. doi: 10.1083/jcb.202408193. Epub 2024 Nov 27. PMID: 39601790; PMCID: PMC11602657.

2024

Garg A, Xing C, Agarwal AK, Westfall AK, Tomchick DR, Zhang X, Xing M, Brown RJ “Gain of function NOTCH3 variants cause familial partial lipodystrophy due to activation of senescence pathways.” Diabetes. 2024 Dec 9:db240624. doi: 10.2337/db24-0624. Epub ahead of print. PMID: 39652711.

Singla A, Boesch DJ, Joyce Fung HY, Ngoka C, Enriquez AS, Song R, Kramer DA, Han Y, Juneja P, Billadeau DD, Bai X, Chen Z, Turer EE, Burstein E, Chen B. "Structural basis for Retriever-SNX17 assembly and endosomal sorting." Nat Commun. 2024 Nov 25;15(1):10193. doi: 10.1038/s41467-024-54583-6. PMID: 38559023; PMCID: PMC10980035.

Hudman-Wing CE, Fung HYJ, Cagatay T, Kwanten B, Niesman AB, Gharghabi M, Permentier B, Shakya B, Shacham S, Landesman Y, Lapalombella R, Daelemans D, Chook YM. "Allosteric degraders induce CRL5 ^ASB8 mediated degradation of XPO1." bioRxiv [Preprint]. 2024 Oct 11:2024.10.07.617049. doi: 10.1101/2024.10.07.617049. PMID: 39416201; PMCID: PMC11482989.

Hu Y, Lopez VA, Xu H, Pfister JP, Song B, Servage KA, Sakurai M, Jones BT, Mendell JT, Wang T, Wu J, Lambowitz AM, Tomchick DR, Pawłowski K, Tagliabracci VS “Biochemical and structural insights into a 5' to 3' RNA ligase reveal a potential role in tRNA ligation.” Proc Natl Acad Sci U S A 121:e2408249121. doi: 10.1073/pnas.2408249121. PMID: 39388274 PMCID: PMC11494293.

Fonda BD, Kato M, Li Y, Murray DT. “Cryo-EM and Solid State NMR Together Provide a More Comprehensive Structural Investigation of Protein Fibrils.” Protein Sci. 2024 Oct;33(10):e5168. doi: 10.1002/pro.5168. PMID: 38853912; PMCID: PMC11160737.

Gan N, Han Y, Zeng W, Jiang Y. "TRPML1 gating modulation by allosteric mutations and lipids." Elife. 2024 Oct 14;13:RP100987. doi: 10.7554/eLife.100987. PMID: 39005349; PMCID: PMC11245044.

Ansari S, Lagasca D, Dumarieh R, Xiao Y, Krishna S, Li Y, Frederick KK. "In cell NMR reveals cells selectively amplify and structurally remodel amyloid fibrils." bioRxiv [Preprint]. 2024 Sep 10:2024.09.09.612142. doi: 10.1101/2024.09.09.612142. PMID: 39314304; PMCID: PMC11419106.

Lawong A, Gahalawat S, Ray S, Ho N, Han Y, Ward KE, Deng X, Chen Z, Kumar A, Xing C, Hosangadi V, Fairhurst KJ, Tashiro K, Liszczak G, Shackleford DM, Katneni K, Chen G, Saunders J, Crighton E, Casas A, Robinson JJ, Imlay LS, Zhang X, Lemoff A, Zhao Z, Angulo-Barturen I, Jiménez-Díaz MB, Wittlin S, Campbell SF, Fidock DA, Laleu B, Charman SA, Ready JM, Phillips MA. “Identification of potent and reversible piperidine carboxamides that are species-selective orally active proteasome inhibitors to treat malaria.” Cell Chem Biol. 2024 Aug 15;31(8):1503-1517.e19. doi: 10.1016/j.chembiol.2024.07.001. Epub 2024 Jul 30. PMID: 39084225.

Fung HYJ, Mittal SR, Niesman AB, Jiou J, Shakya B, Yoshizawa T, Cansizoglu AE, Rout MP, Chook YM. “Phosphate-dependent nuclear export via a novel NES class recognized by exportin Msn5.” bioRxiv [Preprint]. 2024 Aug 12:2024.08.12.607649. doi: 10.1101/2024.08.12.607649. PMID: 39211127; PMCID: PMC11361136.

Li C, Sun XN, Funcke JB, Vanharanta L, Joffin N, Li Y, Prasanna X, Paredes M, Joung C, Gordillo R, Vörös C, Kulig W, Straub L, Chen S, Velasco J, Cobb A, Padula D, Wang MY, Onodera T, Varlamov O, Li Y, Liu C, Nawrocki AR, Zhao S, Oh DY, Wang ZV, Goodman JM, Wynn RM, Vattulainen I, Han Y, Ikonen E, Scherer PE. “Adipogenin Dictates Adipose Tissue Expansion by Facilitating the Assembly of a Dodecameric Seipin Complex.” bioRxiv [Preprint]. 2024 Jul 26:2024.07.25.605195. doi: 10.1101/2024.07.25.605195. PMID: 39211078; PMCID: PMC11360994.

Fernandez-Ramirez MDC, Nguyen BA, Singh V, Afrin S, Evers B, Basset P, Wang L, Pękała M, Ahmed Y, Singh P, Canepa J, Wosztyl A, Li Y, Saelices L. “Multi-organ structural homogeneity of amyloid fibrils in ATTRv-T60A amyloidosis patients, revealed by Cryo-EM.” bioRxiv [Preprint]. 2024 May 14:2024.05.14.594218. doi: 10.1101/2024.05.14.594218. PMID: 38798519; PMCID: PMC11118364.

Embry A, Baggett NS, Heisler DB, White A, de Jong MF, Kocsis BL, Tomchick DR, Alto NM, Gammon DB. “Exploiting bacterial effector proteins to uncover evolutionarily conserved antiviral host machinery.” PLoS Pathog. 2024 May 16;20(5):e1012010. doi: 10.1371/journal.ppat.1012010. eCollection 2024 May. PMID: 38752575. PMCID: PMC11098378.

Nguyen BV, Özden C, Dong K, Torres-Ocampo AP, Dziedzic N, Flaherty D, Huang J, Sankura S, Abromson NL, Tomchick DR, Chen J, Garman SC, Stratton M. “A domain-swapped CaMKII conformation facilitates linker-mediated allosteric regulation.” bioRxiv [Preprint] 2024 Mar27:2024.03.24.586494 doi:10.1101/2024.03.24.586494. PMID: 38585726; PMCID: PMC10996533.

Ahmed MS, Nguyen NUN, Nakada Y, Hsu C-C, Farag A, Lam N, Wang P, Thet S, Menendez-Montes I, Lou X, Secco I, Tomczyk M, Zentilin L, Pei J, Cui M, Walcott G, Tomchick DR, Grishin NV, Xing C, Giacca M, Zhang J, Sadek HA “Identification of FDA-approved drugs that induce heart regeneration in mammals.” Nature Cardiov Res 3:372-388. doi:10.1038/s44161-024-00450-y PMID: 39183959, PMCID: PMC11343477.

Peng W, Garcia N, Servage KA, Kohler JJ, Ready J, Tomchick DR, Fernandez J, Orth K. "Pseudomonas effector AvrB is a glycosyltransferase that rhamnosylates plant guardee protein RIN4." Sci Adv. 2024 Feb 16;10(7);eadd5108. doi: 10.1126/sciadv.add5108. Epub 2024 Feb 14. PMID: 38354245; PMCID: PMC10598227.

2023

Pan Y-Z, Liang Q, Tomchick DR, DeBrabander JK, Rizo J. “Structural insights for selective disruption of Beclin 1 binding to Bcl-1.” Commun Biol. 2023 Oct 24;6(1):1080. doi: 10.1038/s42003-023-05467-w. PMID: 37875561; PMCID: PMC10598227.

Xue, J., Zeng, W., Han, Y., John, S., Ottolia, M., Jiang, Y. "Structural mechanisms of the human cardiac sodium-calcium exchanger NCX1." Nat Commun. 2023 Oct;14(1):6181. doi: 10.1038/s41467-023-41885-4. Epub 2023 Oct 4. PMID: 37794011.

Zhang, J., Zeng, W., Han, Y., Lee, W-R., Liou, J., Jiang, Y. "Lysosomal LAMP proteins regulate lysosomal pH by direct inhibition of the TMEM175 channel." Mol Cell. 2023 July;83(14):2524-2539.e7. doi: 10.1016/j.molcel.2023.06.004.

Boesch DJ, Singla A, Han Y, Kramer DA, Liu Q, Suzuki K, Juneja P, Zhao X, Long X, Medlyn MJ, Billadeau DD, Chen Z, Chen B, Burstein E."Structural Organization of the Retriever-CCC Endosomal Recycling Complex."Nat Struct Mol Biol. 2023 Dec 7;: PMID: 37333304; PMCID: PMC10274727.

Singh, A.K., Kumar, R., Mukherjee, S., Kumar, J., Conlon, K.P., Basrur, V., Chen, Z., Han, X., and Venuprasad, K."RORgt-Raftlin1 complex regulates the pathogenicity of Th17 cells and intestinal inflammation." Nat Commun. 2023 Aug;14(1):4972. doi: 10.1038/s41467-023-40622-1.

Lampea, J.B., Desaia, P.P., Tripathia, A.K., Sabnisa, N.A., Chen, Z., Ranjana, A.P. and Vishwanatha, J.K."Cabazitaxel-Loaded Nanoparticles Reduce the Invasiveness in Metastatic Prostate Cancer Cells: Beyond the Classical Taxane Function." pharmaceutics. 2023 Feb;15(2), 662. doi: 10.3390/pharmaceutics15020662.

Li L, Nguyen BA, Mullapudi V, Li Y, Saelices L, Joachimiak LA. "Disease-associated patterns of acetylation stabilize tau fibril formation." Structure. 2023 Sep 7;31(9):1025-1037.e4. doi: 10.1016/j.str.2023.05.020. Epub 2023 Jun 21. PMID: 37348495; PMCID: PMC10527703.

Zou AJ, Kinch L, Chimalapati S, Garcia N, Tomchick DR, Orth K. "Molecular determinants for differential activation of the bile acid receptor from the pathogen Vibrio parahaemolyticus." J Biol Chem. 2023 Apr;299(4):104591. doi: 10.1016/j.jbc.2023.104591. Epub 2023 Mar 7. PMID: 36894018; PMCID: PMC10140157.

2022

Gan, N., Han, Y., Zeng, W., Wang, Y., Xue, J., Jiang, Y."Structural mechanism of allosteric activation of TRPML1 by PI(3,5)P2 and rapamycin." PNAS. 2022 Feb;119 (7), e2120404119.doi: 10.1073/pnas.2120404119.

Xue, J., Han, Y., Zeng, W., Jiang, Y."Structural mechanisms of assembly, permeation, gating, and pharmacology of native human rod CNG channel." Neuron. 2022 Jan;110 (1), 86-95. e5.doi: 10.1016/j.neuron.2021.10.006.

Russo TA, Umland TC, Deng X, El Mazouni F, Kokkonda S, Olson R, Carlino-MacDonald U, Beanan J, Alvarado CL, Tomchick DR, Hutson A, Chen H, Posner B, Rathod PK, Charman SA, Phillips MA. "Repurposed dihydroorotate dehydrogenase inhibitors with efficacy against drug-resistant Acinetobacter baumannii." Proc Natl Acad Sci U S A. 2022 Dec 20;119(51):e2213116119. doi: 10.1073/pnas.2213116119. Epub 2022 Dec 13. PMID: 36512492; PMCID: PMC9907071.

Chintapula U, Yang S, Nguyen T, Li Y, Jaworski J, Dong H, Nguyen KT. "Supramolecular Peptide Nanofiber/PLGA Nanocomposites for Enhancing Pulmonary Drug Delivery." ACS Appl Mater Interfaces. 2022 Dec 28;14(51):56498-56509.

Adduri RSR, Vasireddy R, Mroz MM, Bhakta A, Li Y, Chen Z, Miller JW, Velasco-Alzate KY, Gopalakrishnan V, Maier LA, Li L, Konduru NV. "Realistic biomarkers from plasma extracellular vesicles for detection of beryllium exposure." Int Arch Occup Environ Health. 2022 Oct;95(8):1785-1796. doi: 10.1007/s00420-022-01871-7. Epub 2022 May 12. PMID: 35551477; PMCID: PMC9489591.

Bernardes NE, Fung HYJ, Li Y, Chen Z, Chook YM. "Structure of IMPORTIN-4 bound to the H3-H4-ASF1 histone-histone chaperone complex." Proc Natl Acad Sci U S A. 2022 Sep 20;119(38):e2207177119. doi: 10.1073/pnas.2207177119. Epub 2022 Sep 14. PMID: 36103578; PMCID: PMC9499513.

Park GJ, Osinski A, Hernandez G, Eitson JL, Majumdar A, Tonelli M, Henzler-Wildman K, Pawłowski K, Chen Z, Li Y, Schoggins JW, Tagliabracci VS. "The mechanism of RNA capping by SARS-CoV-2." Nature. 2022 Sep;609(7928):793-800. doi: 10.1038/s41586-022-05185-z. Epub 2022 Aug 9. PMID: 35944563; PMCID: PMC9492545.

Dewangan PS, Beraki TG, Paiz EA, Appiah Mensah D, Chen Z, Reese ML. "Divergent kinase WNG1 is regulated by phosphorylation of an atypical activation sub-domain." Biochem J. 2022 Sep 16;479(17):1877-1889. doi: 10.1042/BCJ20220076. PMID: 35938919.

Gao H, Li F, Ji Z, Shi Z, Li Y, Yu H. "Cryo-EM structures of human p97 double hexamer capture potentiated ATPase-competent state." Cell Discov. 2022 Feb 22;8(1):19. doi: 10.1038/s41421-022-00379-1. PMID: 35190543; PMCID: PMC8861141.

2021

Strand A, Shen ST, Tomchick DR, Wang J, Wang CR, Deisenhofer J. "Structure and dynamics of major histocompatibility class Ib molecule H2-M3 complexed with mitochondrial-derived peptides." J Biomol Struct Dyn. 2021 Jun 28:1-13. doi: 10.1080/07391102.2021.1942214. Epub ahead of print. PMID: 34176438; PMCID: PMC8722451

Osinski A, Black MH, Pawłowski K, Chen Z, Li Y, Tagliabracci VS. "Structural and mechanistic basis for protein glutamylation by the kinase fold." Mol Cell. 2021 Nov 4;81(21):4527-4539.e8. doi: 10.1016/j.molcel.2021.08.007. Epub 2021 Aug 17. PMID: 34407442; PMCID: PMC8571041

Hsieh TS, Lopez VA, Black MH, Osinski A, Pawłowski K, Tomchick DR, Liou J, Tagliabracci VS. "Dynamic remodeling of host membranes by self-organizing bacterial effectors." Science 2021 May 28; 372(6545):935-941. doi: 10.1126/science.aay8118. Epub 2021 Apr 29. PMID: 33927055; PMCID: PMC8543759

Palmer MJ, Deng X, Watts S, Krilov G, Gerasyuto A, Kokkonda S, El Mazouni F, White J, White KL, Striepen J, Bath J, Schindler KA, Yeo T, Shackleford DM, Mok S, Deni I, Lawong A, Huang A, Chen G, Wang W, Jayaseelan J, Katneni K, Patil R, Saunders J, Shahi SP, Chittimalla R, Angulo-Barturen I, Jiménez-Díaz MB, Wittlin S, Tumwebaze PK, Rosenthal PJ, Cooper RA, Aguiar ACC, Guido RVC, Pereira DB, Mittal N, Winzeler EA, Tomchick DR, Laleu B, Burrows JN, Rathod PK, Fidock DA, Charman SA, Phillips MA. "Potent Antimalarials with Development Potential Identified by Structure-Guided Computational Optimization of a Pyrrole-Based Dihydroorotate Dehydrogenase Inhibitor Series." J Med Chem. 2021 May 13;64(9):6085-6136. doi: 10.1021/acs.jmedchem.1c00173. Epub 2021 Apr 20. PMID: 33876936; PMCID: PMC8171248

Li B, Deng X, Kim SH, Buhrow L, Tomchick DR, Phillips MA, Michael AJ. "Alternative pathways utilize or circumvent putrescine for biosynthesis of putrescine-containing rhizoferrin." J Biol Chem. 2021 Jan-Jun;296:100146. doi: 10.1074/jbc.RA120.016738. Epub 2020 Dec 10. PMID: 33277357; PMCID: PMC7857480

2020

Li F, Li Y, Ye X, Gao H, Shi Z, Luo X, Rice LM, Yu H. “Cryo-EM structure of VASH1-SVBP bound to microtubules.” Elife. 2020 Aug 10;9:e58157. doi: 10.7554/eLife.58157. PMID: 32773040; PMCID: PMC7449697.

Peng W, Casey AK, Fernandez J, Carpinone EM, Servage KA, Chen Z, Li Y, Tomchick DR, Starai VJ, Orth K "A distinct inhibitory mechanism of the V-ATPase by Vibrio VopQ revealed by cryo-EM." Nat Struct Mol Biol. 2020 Jun;27(6):589-597. doi: 10.1038/s41594-020-0429-1. Epub 2020 May 18. PMID: 32424347

Jiao L, Shubbar M, Yang X, Zhang Q, Chen S, Wu Q, Chen Z, Rizo J, Liu X. "A partially disordered region connects gene repression and activation functions of EZH2." Proc Natl Acad Sci U S A. 2020 Jul 21;117(29):16992-17002. doi: 10.1073/pnas.1914866117. Epub 2020 Jul 6. PMID: 32631994; PMCID: PMC7382310

Kokkonda S, Deng X, White KL, El Mazouni F, White J, Shackleford DM, Katneni K, Chiu FCK, Barker H, McLaren J, Crighton E, Chen G, Angulo-Barturen I, Jimenez-Diaz MB, Ferrer S, Huertas-Valentin L, Martinez-Martinez MS, Lafuente-Monasterio MJ, Chittimalla R, Shahi SP, Wittlin S, Waterson D, Burrows JN, Matthews D, Tomchick D, Rathod PK, Palmer MJ, Charman SA, Phillips MA. "Lead Optimization of a Pyrrole-Based Dihydroorotate Dehydrogenase Inhibitor Series for the Treatment of Malaria." J Med Chem. 2020 May 14;63(9):4929-4956. doi: 10.1021/acs.jmedchem.0c00311. Epub 2020 Apr 16. PMID: 32248693; PMCID: PMC7394244

Sreelatha A, Nolan C, Park BC, Pawłowski K, Tomchick DR, Tagliabracci VS. "A Legionella effector kinase is activated by host inositol hexakisphosphate." J Biol Chem. 2020 May 1;295(18):6214-6224. doi: 10.1074/jbc.RA120.013067. Epub 2020 Mar 30. PMID: 32229585; PMCID: PMC7196655

Zhong X, Su L, Yang Y, Nair-Gill E, Tang M, Anderton P, Li X, Wang J, Zhan X, Tomchick DR, Brautigam CA, Moresco EMY, Choi JH, Beutler B. "Genetic and structural studies of RABL3 reveal an essential role in lymphoid development and function." Proc Natl Acad Sci U S A. 2020 Apr 14;117(15):8563-8572. doi: 10.1073/pnas.2000703117. Epub 2020 Mar 27. PMID: 32220963; PMCID: PMC7165429